We have developed databases and software useful for comparative analysis of protein three-dimensional structure. These tools are distributed freely to biologists and developers of biotechnology software. MMDB (Molecular Modeling DataBase) is the 3D-structure component of the Entrez molecular biology retrieval system. MMDB is an ASN.1 database where all data items describing macromolecular structure are validated and explicitly listed, so that application software need not contain the complex logic required to retrieve this information from text formats such as PDB files. Ongoing curatorial work has added of accurate taxonomy assignments for macromolecular structures within MMDB. Ongoing software development has added new message and data types for transmission of structure-structure alignment data to local viewers, and a highly automated monthly update and indexing system, Pubstruct. Cn3D ("see in three dimensions") is a multi-structure visualization program distributed as part to the Entrez client software and in a stand-alone version launched via the MIME protocol in World-Wide-Web Entrez. The software differs from other public domain viewers in supporting display of multiple aligned structures from Entrez's "structure neighbor" database, and in supporting simultaneous highlighting/picking of multiple sequence and multiple structure alignments. Other features are on-the-fly alignment of the sequences of homologs, so that an Entrez user may easily map conserved sequence features onto the known 3D structure. To facilitate molecular biologist's identification of important structure-function relationships within protein families we have added core-structure alignment editing and threading tools to Cn3D's sequence display windows, a feature which also supports curation of CDD (a Conserved Domain Database). The latest version also provides greatly improved molecular graphics performance on popular computing platforms. As of October, 2004, over 250,000 copies of CN3D have been downloaded. A new "related structures" link has been added to NCBI BLAST servers this year, to provide easy-to use mapping to 3D structure whenever possible. This is based on a continuously updated database of pre-computed BLAST alignments of protein sequences in the Entrez/PubMed system with all protein structures to which they are similar. Future development will consider user of more accurate structure-based alignment methods. A completely re-engineered version of the Conserved Domain Architecture Research Tool (CDART) database has also been developed this year. It provides domain annotations derived from the Conserved Domain Database for MMDB protein structure displays as well as domain annotation for all protein sequences in the Entrez/Pubmed retrieval system.